Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

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	Gene Summary
	Phenotypic Information (metabolism pathway, cancer, disease, phenome)
	Mutations : SVs, CNVs, SNVs
	Gene expression: GE, Protein, DEGE, CNV vs GE
	Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG
	Pharmacological Information: Drug-Gene Network
	Cross referenced IDs

Gene Summary for MTHFD1

Basic gene info.	Gene symbol	MTHFD1
	Gene name	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetase
	Synonyms	MTHFC\|MTHFD
	Cytomap	UCSC genome browser: 14q24
	Genomic location	chr14 :64854758-64926725
	Type of gene	protein-coding
	RefGenes	NM_005956.3,
	Ensembl id	ENSG00000100714
	Description	5,10-methylenetetrahydrofolate dehydrogenase, 5,10-methylenetetrahydrofolate cyclohydrolase, 10-formyltetrahydrofolate synthetaseC-1-tetrahydrofolate synthase, cytoplasmicC1-THF synthasecytoplasmic C-1-tetrahydrofolate synthase
	Modification date	20141207
dbXrefs	MIM : 172460
	HGNC : HGNC
	Ensembl : ENSG00000100714
	HPRD : 01403
	Vega : OTTHUMG00000141309
Protein	UniProt: P11586 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_MTHFD1
	BioGPS: 4522
	Gene Expression Atlas: ENSG00000100714
	The Human Protein Atlas: ENSG00000100714
Pathway	NCI Pathway Interaction Database: MTHFD1
	KEGG: MTHFD1
	REACTOME: MTHFD1
	ConsensusPathDB
	Pathway Commons: MTHFD1
Metabolism	MetaCyc: MTHFD1
	HUMANCyc: MTHFD1
Regulation	Ensembl's Regulation: ENSG00000100714
	miRBase: chr14 :64,854,758-64,926,725
	TargetScan: NM_005956
	cisRED: ENSG00000100714
Context	iHOP: MTHFD1
	cancer metabolism search in PubMed: MTHFD1
	UCL Cancer Institute: MTHFD1
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of MTHFD1 in cancer cell metabolism	1. Cheng TYD, Makar KW, Neuhouser ML, Miller JW, Song X, et al. (2015) Folate‐mediated one‐carbon metabolism genes and interactions with nutritional factors on colorectal cancer risk: Women's Health Initiative Observational Study. Cancer. go to article

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Phenotypic Information for MTHFD1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: MTHFD1
	Familial Cancer Database: MTHFD1

* This gene is included in those cancer gene databases.


Oncogene ¹	Tumor Suppressor gene ²	Cancer Gene Census ³	CancerGenes ⁴	Network of Cancer Gene ⁵	Significant driver gene in	Therapeutic Vulnerabilities in Cancer¹

cf) number; DB name
1 Oncogene; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
2 Tumor Suppressor gene; https://bioinfo.uth.edu/TSGene/,
3 Cancer Gene Census; http://www.nature.com/nrc/journal/v4/n3/abs/nrc1299.html,
4 CancerGenes; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
5 Network of Cancer Gene; http://ncg.kcl.ac.uk/index.php,
1Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

Metabolic Pathway Description
KEGG_GLYOXYLATE_AND_DICARBOXYLATE_METABOLISM REACTOME_METABOLISM_OF_VITAMINS_AND_COFACTORS

Others
OMIM	114500; phenotype. 172460; gene+phenotype. 601634; phenotype.
Orphanet	268377; Total spina bifida aperta. 268384; Thoracolumbosacral spina bifida aperta. 268388; Lumbosacral spina bifida aperta. 268392; Cervical spina bifida aperta. 268397; Cervicothoracic spina bifida aperta. 268740; Upper thoracic spina bifida aperta. 268748; Total spina bifida cystica. 268752; Thoracolumbosacral spina bifida cystica. 268758; Lumbosacral spina bifida cystica. 268762; Cervical spina bifida cystica. 268766; Cervicothoracic spina bifida cystica. 268770; Upper thoracic spina bifida cystica.
Disease	KEGG Disease: MTHFD1
	MedGen: MTHFD1 (Human Medical Genetics with Condition)
	ClinVar: MTHFD1
Phenotype	MGI: MTHFD1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: MTHFD1

Mutations for MTHFD1

* Under tables are showing count per each tissue to give us broad intuition about tissue specific mutation patterns.You can go to the detailed page for each mutation database's web site.

Structural Variants in COSMIC : go to COSMIC mutation histogram

There's no structural variation information in COSMIC data for this gene.

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows MTHFD1 related fusion information.

ID	Head Gene						Tail Gene
Accession	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a
BG955100	MTHFD1	11	197	14	64886895	64887081	LOC100505782	193	334	17	39565582	39565720
BG180332	GLT25D1	1	203	19	17692507	17692709	MTHFD1	196	672	14	64912837	64913313
W27097	MTHFD1	25	122	14	64915420	64915518	MTHFD1	114	432	14	64915015	64915329
BE707197	MTHFD1	5	72	14	64905812	64905879	UVRAG	67	432	11	75852850	75853215
AW581578	PIGC	9	124	1	172410948	172411063	MTHFD1	107	304	14	64924985	64926633
BG992574	PRRC2C	15	400	1	171561993	171562378	MTHFD1	392	517	14	64915129	64915254

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

LOSS (# sample)

cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract)

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SNV Counts per Each Loci in COSMIC data : go to COSMIC point mutation

: Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=55)	Stat. for Synonymous SNVs (# total SNVs=13)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=0)
There's no deleted snv.	There's no inserted snv.

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Top 10 SNVs Having the Most Samples in COSMIC data

* When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site,primary_histology,mutation(aa),pubmedID.

GRCh37 position	Mutation(aa)	Unique sampleID count
chr14:64908845-64908845	p.R653Q	3
chr14:64892515-64892515	p.N308T	2
chr14:64886575-64886575	p.E220G	2
chr14:64902374-64902374	p.I528V	2
chr14:64921543-64921543	p.D890N	2
chr14:64898264-64898264	p.L442L	2
chr14:64914970-64914970	p.L738F	2
chr14:64921552-64921552	p.A893T	2
chr14:64898312-64898312	p.A458A	2
chr14:64884707-64884707	p.T194P	2

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SNV Counts per Each Loci in TCGA data

: non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=2

Point Mutation/ Tissue ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	3	5		12	1		2		4	1		1	6	2		1	10	4	2	9
# mutation	3	5		12	1		2		4	1		1	6	2		1	11	4	2	9
nonsynonymous SNV	2	4		9	1		1		3	1		1	5	2		1	7	3	2	6
synonymous SNV	1	1		3			1		1				1				4	1		3

cf) Tissue ID; Tissue type (1; BLCA[Bladder Urothelial Carcinoma], 2; BRCA[Breast invasive carcinoma], 3; CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], 4; COAD[Colon adenocarcinoma], 5; GBM[Glioblastoma multiforme], 6; Glioma Low Grade, 7; HNSC[Head and Neck squamous cell carcinoma], 8; KICH[Kidney Chromophobe], 9; KIRC[Kidney renal clear cell carcinoma], 10; KIRP[Kidney renal papillary cell carcinoma], 11; LAML[Acute Myeloid Leukemia], 12; LUAD[Lung adenocarcinoma], 13; LUSC[Lung squamous cell carcinoma], 14; OV[Ovarian serous cystadenocarcinoma ], 15; PAAD[Pancreatic adenocarcinoma], 16; PRAD[Prostate adenocarcinoma], 17; SKCM[Skin Cutaneous Melanoma], 18:STAD[Stomach adenocarcinoma], 19:THCA[Thyroid carcinoma], 20:UCEC[Uterine Corpus Endometrial Carcinoma])

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Top 10 SNVs Having the Most Samples in TCGA data

* We represented just top 10 SNVs. When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site, primary_histology, mutation(aa), pubmedID.

Genomic Position	Mutation(aa)	Unique sampleID count
chr14:64886575	p.S79C	2
chr14:64898264	p.E628D	2
chr14:64879239	p.L442L	2
chr14:64908171	p.E220G	2
chr14:64855180	p.T469T	1
chr14:64898551	p.S688S	1
chr14:64921592	p.V904V	1
chr14:64882205	p.V253L	1
chr14:64908830	p.F489Y	1
chr14:64894152	p.P692R	1

Other DBs for Point Mutations

Point Mutation Table of Ensembl: go to Ensembl variation table

Mutation of cBioPortal: go to cBioPortal's Cross-cancer alteration summary

Copy Number for MTHFD1 in TCGA

* Copy number data were extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered on Jan-05-2015. Function ProcessCNAData in TCGA-Assembler package was used to obtain gene-level copy number value which is calculated as the average copy number of the genomic region of a gene.

cf) Tissue ID[Tissue type]: BLCA[Bladder Urothelial Carcinoma], BRCA[Breast invasive carcinoma], CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], COAD[Colon adenocarcinoma], GBM[Glioblastoma multiforme], Glioma Low Grade, HNSC[Head and Neck squamous cell carcinoma], KICH[Kidney Chromophobe], KIRC[Kidney renal clear cell carcinoma], KIRP[Kidney renal papillary cell carcinoma], LAML[Acute Myeloid Leukemia], LUAD[Lung adenocarcinoma], LUSC[Lung squamous cell carcinoma], OV[Ovarian serous cystadenocarcinoma ], PAAD[Pancreatic adenocarcinoma], PRAD[Prostate adenocarcinoma], SKCM[Skin Cutaneous Melanoma], STAD[Stomach adenocarcinoma], THCA[Thyroid carcinoma], UCEC[Uterine Corpus Endometrial Carcinoma]

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Gene Expression for MTHFD1

Gene Expression in Cancer Cell-lines (CCLE)

* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data.

Differential Gene Expression in Primary Tumors (TCGA)

* Normalized gene expression data of RNASeqV2 was extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered at Jan-05-2015. Only eight cancer types have enough normal control samples for differential expression analysis.
(t test, adjusted p<0.05 (using Benjamini-Hochberg FDR))

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CNV vs Gene Expression Plot

* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types

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Gene-Gene Network Information

Co-Expressed gene's network Plot

* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types


AMD1,ANKS6,CDC20,CTPS1,EXO5,COLGALT1,HMGA1, IFRD1,MPP6,MTHFD1L,NIP7,NUP93,PABPC4,PLEKHG1, PPP1R14C,PSAT1,TBPL1,ULBP1,YARS,YBX1,ZFP69B	ADORA3,C1RL,CASP4,EXOG,FAM20A,FAM57A,IFI16, LOC541471,LYN,MTHFD1L,MYD88,OSMR,RASSF2,SAMSN1, SELPLG,SLCO2B1,SULF2,TMEM173,TPM4,TUBA1B,UBASH3B

CAD,CCDC86,CDCA5,CTPS1,EFTUD2,LMNB2,MCM4, MTHFD1L,NCAPD3,NCL,NLE1,NOLC1,POLR1A,SLC7A5, SSRP1,STC2,TCP1,TRAP1,XPO5,XPOT,YARS	CALR,CRELD2,DNAJC10,GARS,HM13,HSP90B1,HSPA5, HYOU1,IARS,IPO4,LRP8,MANF,MARS,MCM6, MTHFD1L,PDIA4,PKM,RUVBL1,SLC38A5,SRM,YARS

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

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Pharmacological Information for MTHFD1

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	P11586; -.
Chemistry	ChEMBL	CHEMBL2541; -.
Organism-specific databases	PharmGKB	PA31236; -.
Organism-specific databases	CTD	4522; -.

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB00116	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetase	approved; nutraceutical	Tetrahydrofolic acid
DB00157	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetase	approved; nutraceutical	NADH
DB02358	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetase	experimental	LY374571
DB03461	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetase	experimental	2'-Monophosphoadenosine 5'-Diphosphoribose
DB04322	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetase	experimental	LY249543
DB00145	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetase	approved; nutraceutical	Glycine
DB00133	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetase	approved; nutraceutical	L-Serine
DB00158	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetase	approved; nutraceutical	Folic Acid
DB00563	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetase	approved	Methotrexate

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Cross referenced IDs for MTHFD1

* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section

: Open all cross reference information